Abstract: Pot culture experiment was conducted with a yellow brown earth collected from Xinzhou, Wuhan, Hubei, China, to study the effect of molybdenum and nitrogen fertilizers on free amino acid, protein and its amino acid composition of winter wheat grains The main results were showed as follows: the contents of protein, albumin, prolamine, protein amino acid and its compositions, and the percentages of the glutamic and proline to total amino acid were all increased, but the contents and percentages of free aspartic acid and threonine in wheat flour were decreased by nitrogen fertilizer application regardless of molybdenum utilization The content of free amino acid in wheat flour was raised by increasing rate of nitrogen application without molybdenum, and decreased with molybdenum application Even though there was no effect of molybdenum application on content of protein in wheat grains, the ratio and content of low molecular weight protein was reduced and the high ones was increased by molybdenum utilization, and a large quantity of free amino acid particularly the hydrophilic amino acid was accumulated in grains of molybdenum deficient wheat, whether the application rate of nitrogen fertilizer was high or low The accumulations of low molecular weight protein, free amino acid and the hydrophilic ones in grains of molybdenum deficient wheat especially with the high rate of nitrogen application might be the main reason of low seed dormancy of wheat induced by molybdenum deficiency